title: Control in vivo - 3


title: GUEucXylem_TimeSeries_Slide49

status: Public on May 13 2009

type: RNA

city: Pretoria

first: Owen

middle: Luke

last: Solomon

state: Gauteng

address: Lab 6-20, Agricultural Building, University of Pretoria, Lynwood Rd

department: Genetics

country: South Africa

institute: University of Pretoria

hyb_protocol: Equal quantities of dye were mixed for each channel and dried in a vacuum centrifuge. Dried probes were resuspended in 60ul of hyb buffer (50%formamide, 5xSSC, 0.5%SDS, 5x Denhardt's solution, 0.5ug/ul poly d(A) and 0.5ug/ul calf thymus DNA). Denaturation for 3mins at 95C, cooled on ice and applied to pre hybridised slide and covered with cover slip. Slides were prehybridised in a (5x SSC, 1%BSA, 0.1xSDS) solution, at 42C for 45mins. Rinsed twice in water and once in isopropanol and spun dry. Scans were hybridised overnight in a water bath at 42C overnight. Post hyb washes were once in (1xSSC, 0.2%SDS at 42C) once in (0.1xSSC, 0.2%SDS at room temp) and three times in (0.1%SDS at room temp). Slides were dried and scanned within the hour.

scan_protocol: Slides were scanned on a Genepix™ 4000B scanner (Axon Instruments, Foster City, CA). Laser and photomultiplier settings were adjusted to obtain a signal ratio of 1:1 between the two dyes. Image analysis was performed with GenePix Pro 5.0 (Axon Instruments, Foster City, CA). Intensities were calculated for each spot, and spots affected by dust specks or high local background were manually flagged and removed from subsequent analysis.

data_processing: Raw signal intensity values (not background corrected) for each channel were transformed (log2) and the four replicate spots for each target on a single slide were averaged. The ratio of the transformed and averaged Cy3 and Cy5 values was then computed for each target.

molecule: total RNA

organism: Eucalyptus grandis x Eucalyptus urophylla

label_protocol: aminoallyl labeled cDNA was prepared from 15ug total RNA using SuperScript III RT primed with random hexamers. cDNA was purified and labelled with Cy3, and excess dye removed using a Qiagen PCR Purification Kit as in TIGR protocol #M0004.

extract_protocol: CTAB method of Zeng and Yang (2002)

treatment_protocol: Stored at -80C

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 18:00.

label_protocol: aminoallyl labeled cDNA was prepared from 15ug total RNA using SuperScript III RT primed with random hexamers. cDNA was purified and labelled with Cy5, and excess dye removed using a Qiagen PCR Purification Kit as in TIGR protocol #M0004.

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 06:00.


title: GUEucXylem_TimeSeries_Slide46

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 15:00.


title: Martin_0d_rep2

city: Aleppo

first: Michael

last: Baum

state: Aleppo

address: ICARDA

department: BIGMP

country: Syria

institute: ICARDA

description: All scanned data from barley 1 GeneChips were processed by robust multiarray average (RMA) (Irizarry et al., 2003) using ArrayAssist software version 3.4 (Stratagene, La Jolla, CA, UAS)

hyb_protocol: Biotin-tagged cRNA was fragmented to strands of 35 to 200 bases in length, and 15 µg of fragmented cRNA was used for each hybridization. Barley 1 GeneChips were hybridized for 16 h at 45°C with rotation in a GeneChip® Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA). The arrays were washed and stained with R-phycoerythrin streptavidin in a Fluidics Station.

scan_protocol: The Arrays were subsequently scanned with Affymetrix GeneChip® Scanner 3000

data_processing:
Normalized expression values were computed from raw CEL files by first applying the RMA model of probe-specific correction of perfect match probes. The algorithm consists of three steps—a model-based background correction stage neutralizes the effects of background noise and the processing artifacts, a subsequent quantile normalization stage aligns expression values to a common scale, and finally, an iterative median polishing procedure summarizes the data and generates a single expression value for each probe set. Resulting RMA expression values were log2-transformed. Average log signal intensity values of three biological replicates for each sample were then computed and these were used for further analysis.  To identify differentially expressed genes, student's t-test was applied with a maximal FDR (false discovery rate) of 5% (Benjamini-Hochberg algorithm).
RMA data for each individual Affymetrix chip not available. Thus the Sample data tables instead report MAS5.0-processed data.  A table of the average, log2 RMA signal intensity values of three biological replicates for each sample is linked as a supplementary file on the GSE15970 record.

label: Biotin

organism: Hordeum vulgare

source_name: Flag leaves, harvested at 0 d after drought stress

label_protocol: 5 µg of high quality total RNA were reverse transcribed using the One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA, USA). The resulting double-stranded cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using Affymetrix IVT Labeling Kit as Expression Analysis Technical Manual (2001, Affymetrix)

extract_protocol: Seven flag leaves of a replication for each genotype were harvested at 0 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).

tag: genotype

value: Martin

tag: trait for drought tolerance

value: drought tolerance

tag: tissue

value: flag leaves

tag: treatment

value: 0 d after drought stress


title: Embryo at Day 1, female biological replicate 2

city: kansas city

first: Sachin

last: Mathur

state: MO

address: 5100 Rockhill Drive

department: School of Computing & Engineering

country: USA

institute: University of Missouri Kansas City

description: chicken embryo at 1 day old

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Standard Affymetrix Scanner

data_processing: The data were analyzed with MAS5 data processing method implemented in Bioconductor-Affy package with 100 as target intensity.

label: biotin

organism: Gallus gallus

source_name: Female

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50ng total RNA.

growth_protocol: HH stage 4- chicken embryos were dissected out of eggs and put on EC culture in humidified incubator for 3 hours at 380C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Primitive streak tissues (400umx400um at 70% to 90% streak level) were dissected out using tungsten needle under dissecting microscope. Tissues were then rinsed in ice cold Tyrode's solution and transfered into the Trizol solution (GibcoBRL). Then they were frozen immediately on dry ice and stored at -80 degrees.

value: Embryo

tag: developmental stage

value: Hamburger-Hamilton stage 4

tag: sex

value: Female

tag: age

value: 1 day


title: GUEucXylem_TimeSeries_Slide50

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 11:00.


title: FAD in vivo - 3

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description:
RNA from fathead minnow ovary exposed in vivo to a 50 ug/L fadrozole
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol)

scan_protocol: The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA)

data_processing: The intensity of each spot was summarized by the median pixel intensity. A log2 transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities (Zahurak et al., 2007). Probes that did not hybridize were removed from consideration.

organism: Pimephales promelas

source_name: Fathead minnow ovary exposed to fadrozole

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit)

growth_protocol: Adult (ca. 6 month old) female FHM from an on-site culture (EPA’s Mid-Continent Ecology Division Laboratory, Duluth) were acclimated to test conditions (25oC, 16:8 light:dark photoperiod, and fed adult brine shrimp twice daily) over a period of one week as described in USEPA (2001).  Exposures were initiated by transferring fish from the acclimation tanks to randomly assigned treatment tanks, n = 6 fish per treatment tank.  Water quality conditions, monitored daily, were maintained within the guidelines established for fathead minnow reproduction tests.

extract_protocol: Total RNA was isolated from gonadal tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Fathead minnow ovary exposed in vitro for 12h to fadrozole, or solvent control

value: ovary

source_name: Reference sample

tag: sample type

value: liver, brain, and gonad pool


title: FAD in vivo - 4


title: Root_Control1

city: Texcoco

first: Marta

middle: Silva

last: Lopes

state: Mexico

address: km 45, carretera Mexico-Veracruz, El Batan, Texcoco

department: wheat physiology

country: Mexico

institute: cimmyt

description: All sample extraction and micro chip manipulation were carried out at PROGENIKA, in SPAIN (Bilbao)

hyb_protocol: Standard Affymetrix procedures.

scan_protocol: Standard Affymetrix procedures.

data_processing: Normalization was carried out in 2 steps: using GeneSpring v7.1 (Agilent) and previously scaled with GCOS.

source_name: Barley roots grown in control conditions

label_protocol: Standard Affymetrix procedures.

growth_protocol: Barley (Hordeum vulgare L. cv. Graphic) seeds were carefully chosen with similar weight, shape and size and sown in 1 L pots containing sand in a glasshouse for 15 days (Experimental Fields of the University of Barcelona) and irrigated with a half strength Hoagland solution containing either 0 µM (control), 500 µM or 1000 µM of HgCl2. Daily means of temperature, relative humidity and maximum irradiance in the glasshouse throughout the experiment were 16ºC, 45% and 378 Wm-2, respectively. For root and shoot dry weight, 5 plantlets were sampled, immediately frozen in liquid nitrogen, lyophylized and dry weights were recorded and shoot to root ratio calculated. Additional three plantlets per treatment (only controls and 1000 μM HgCl2) were sampled and the entire roots were separated from leaves, washed with de-ionized water and immediately frozen in liquid N and kept at -80ºC until use for RNA extractions.

extract_protocol: Trizol reagent and Rneasy Quiagen

value: root

tag: agent

value: control


title: Root_Hg3

source_name: Barley roots exposed to 1000 uM Hg


title: GUEucXylem_TimeSeries_Slide48

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 22:00.


title: GUEucXylem_TimeSeries_Slide47

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 02:00.


title: Moroc9-75_1d_rep2

source_name: Flag leaves, harvested at 1 d after drought stress

extract_protocol: Seven flag leaves of a replication for each genotype were harvested at 1 d after reach 10% of AWC in the soil to constitute a single biological replicate. These flag leaves were employed for RNA isolation by using Trizol reagent following the manufacturer’s protocol (Invitrogen, Karlsruhe, Germany). The RNA was further purified using RNeasy Kit (Qiagen, Hilden, Germany). RNA yield and quality were determined by using an Agilent 2100 Bioanalyzer (Agilent Techologies, Boblingen, Germany).

value: drought tolerance (sensitive)

value: 1 d after drought stress


title: Control in vivo - 1

description:
RNA from fathead minnow control ovary
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

source_name: Fathead minnow control ovary


title: GUEucXylem_TimeSeries_Slide44


title: Root_Hg1


title: GUEucXylem_TimeSeries_Slide45


title: GUEucXylem_TimeSeries_Slide33


title: FAD in vitro - 4

description:
RNA from fathead minnow ovary exposed in vitro to a 50 ug/L fadrozole
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

growth_protocol: Ovaries from 6 replicate fish were sliced into 12±5 mg pieces and randomly distributed across sample culture wells to minimize sample effects due to potential tissue heterogeneity. Ovary slices were incubated in tissue culture medium supplemented with IBMX (0.1 mM), 25-hydroxycholesterol (1ug/ml), and 50 uM FAD, or solvent control (0.07% methanol) for intervals of 1 to 12 hrs. Replicate ovary slices were removed at appropriate times, snap frozen in liquid nitrogen, and stored at -80°C until needed.


title: Control in vitro - 4

description:
RNA from fathead minnow ovary exposed in vitro to solvent control (0.07% methanol)
The reference pool consisted of equal amounts of RNA from control fathead minnow female and male tissues (liver, brain and gonad).
Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

source_name: Fathead minnows control ovary


title: GUEucXylem_TimeSeries_Slide34


title: FAD in vitro - 1

source_name: Fathead minnows ovary exposed to fadrozole


title: Hela mir34b-5p 342409

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
Hela_mirNeg2 vs Hela_mir34b-5p
Date:2008/07/03

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 18 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

organism: Homo sapiens

source_name: Hela mirNeg2

label_protocol: Ambion

extract_protocol: Trizol

tag: sample

tag: cell line

value: Hela

value: uterus

tag: cell type

value: uterine epithelial cells

tag: extract amount (ug)

tag: extract concentration (ng/ul)

source_name: Hela mir34b-5p


title: Hela mir34c 342405

description:
Hela_mirNeg2 vs Hela_mir34c
Date:2008/07/03

source_name: Hela mir34c


title: Control in vitro - 3

source_name: reference sample


title: FAD in vitro - 3


title: Hela mir34a 342408

description:
Hela_mirNeg2 vs Hela_mir34a
Date:2008/07/03

source_name: Hela mir34a


title: Control in vitro - 1


title: FAD in vitro - 2


title: Control in vitro - 2


title: GUEucXylem_TimeSeries_Slide27

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 15:00.


title: Hela mir34a 342410

description:
Hela_mir34a vs Hela_mirNeg2
Date:2008/07/03


title: GUEucXylem_TimeSeries_Slide25


title: Hela mir34b-5p 342675

description:
Hela_mir34b-5p vs Hela_mirNeg2
Date:2008/07/03


title: Hela mir34b-5p 342699

description:
Hela_mirNeg1 vs Hela_mir34b-5p
Date:2008/07/03

source_name: Hela mirNeg1


title: GCEucXylem_TimeSeries_Slide22

organism: Eucalyptus camaldulensis x Eucalyptus grandis

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. camaldulensis clone from 1-2m above ground level. Collected at 02:00.

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. camaldulensis clone from 1-2m above ground level. Collected at 15:00.


title: Adenovirus vector treated animal #1 vs mock treated: 72 hours post-treatment

city: Richmond

first: Paul

last: Fawcett

state: VA

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31832.gif

hyb_protocol: not provided

scan_protocol: GenePix

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Mus musculus

source_name: Mock treated animal liver: 72 hours post-treatment

label_protocol: not provided

extract_protocol: not provided

tag: treatment

value: mock treated - 72 hours post-treatment

tag: tissue

value: liver

source_name: Adenovirus vector treated animal liver: 72 hours post-treatment

value: adenovirus vector treated - 72 hours post-treatment


title: GUEucXylem_TimeSeries_Slide23

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. urophylla clone from 1-2m above ground level. Collected at 06:00.


title: Adenovirus vector treated animal #1 vs mock treated: 6 hours post-treatment

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29227.gif

source_name: Mock treated animal liver: 6 hours post-treatment

value: mock treated - 6 hours post-treatment

source_name: Adenovirus vector treated animal liver: 6 hours post-treatment

value: adenovirus vector treated - 6 hours post-treatment


title: GCEucXylem_TimeSeries_Slide21

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. camaldulensis clone from 1-2m above ground level. Collected at 11:00.

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. camaldulensis clone from 1-2m above ground level. Collected at 18:00.


title: Helper-dependent adenovirus vector treated animal #1 vs mock treated: 6 hours post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29234.gif

source_name: Helper-dependent adenovirus vector treated animal liver: 6 hours post-treatment

value: helper-dependent adenovirus vector treated - 6 hours post-treatment


title: Hela mir34a 342705

description:
Hela_mir34a vs Hela_mirNeg1
Date:2008/07/03


title: Hela mir34a 342697

description:
Hela_mirNeg1 vs Hela_mir34a
Date:2008/07/03


title: Helper-dependent adenovirus vector treated animal #2 vs mock treated: 4 weeks post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30399.gif

source_name: Mock treated animal liver: 4 weeks post-treatment

value: mock treated - 4 weeks post-treatment

source_name: Helper-dependent adenovirus vector treated animal liver: 4 weeks post-treatment

value: helper-dependent adenovirus vector treated - 4 weeks post-treatment


title: GCEucXylem_TimeSeries_Slide20

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. camaldulensis clone from 1-2m above ground level. Collected at 06:00.


title: Hela mir34c 342703

description:
Hela_mir34c vs Hela_mirNeg2
Date:2008/07/03


title: GCEucXylem_TimeSeries_Slide19


title: Hela mir34c 342709

description:
Hela_mir34c vs Hela_mirNeg1
Date:2008/07/03


title: Adeno-associated virus vector treated animal #1 vs mock: 72 hours post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37921.gif

source_name: Adeno-associated virus vector treated animal liver: 72 hours post-treatment

value: adeno-associated virus vector treated - 72 hours post-treatment


title: Hela mir34b-5p 342350

description:
Hela_mir34b vs Hela_mirNeg1
Date:2008/07/03


title: ectopic endometrium (vesical endometriosis)

type: genomic

city: Paris

first: Bruno

last: Borghese

address: 24, rue du Faubourg Saint-Jacques

department: Genetics and Development

institute: Institut Cochin

description:
Methylated DNA immunoprecipitation.
4_VES

hyb_protocol: Samples were shipped to Genpathway Inc. in San Diego and hybridization was performed there according to Affymetrix protocols.

scan_protocol: Samples were shipped to Genpathway Inc. in San Diego and scanning was performed there according to Affymetrix protocols.

data_processing:
A. Affymetrix analysis: Image data from the array scans are analyzed using Affymetrix’ Tiling Analysis Software (TAS). This analysis generates BAR files that contain the intensities for all probes on the arrays. The intensities are expressed either as signals (estimating the fold enrichment in log2 scale) or as p-values (probabilities that measure the significance of the enrichment).
B. Intervals (“Binding or association sites”): Using the threshold selected (based on Affymetrix’  recommendations and known positive and negative genomic regions), Intervals with signals or p-values greater than the threshold are determined and compiled into BED files. Intervals represent the locations of intensity peaks.
C. Active Regions: Active Regions are genomic regions that contain one or more Intervals in close proximity to each other. In Genpathway’s standard analysis, Intervals from different samples need to overlap by at least 1 bp to be added to the same Active Region. Active  Regions are useful to consider because Intervals may not be exactly the same, e.g., in  location or length, when comparing different samples.
D. Annotations: After the Intervals and Active Regions are defined, their exact locations along with their proximities to gene annotations and other genomic features are determined. This data is available in the 'GSE16079_Intervals_ActiveRegions_Annotations.txt' file, which is linked to the GSE16079 record.

molecule: genomic DNA

source_name: deep endometriosis

label_protocol: Samples were shipped to Genpathway Inc. in San Diego and labelling was performed there according to Affymetrix protocols.

growth_protocol: Liquid nitrogen.

extract_protocol: DNA was extracted using the FastDNA(R) SPIN Kit and the FastPrep® Instrument (Qbiogene, Carlsbad, CA).

tag: number of patients

value: Pool of 5 patients

tag: disease

value: endometriotic lesions (vesical endometriosis)

tag: phase of menstrual cycle

value: luteal phase

tag: race

value: Caucasian


title: ectopic endometrium (superficial endometriosis)

description:
Methylated DNA immunoprecipitation.
3_SUP

source_name: superficial endometriosis

value: endometriotic lesions (superficial endometriosis)


title: Hela mir34c 342349

description:
Hela_mirNeg1 vs Hela_mir34c
Date:2008/07/03

tag: sample

tag: cell line

value: Hela


title: GCEucXylem_TimeSeries_Slide16


title: GCEucXylem_TimeSeries_Slide13

tag: Light scrapings of differentiating xylem tissue. Collected from three year old Eucalyptus grandis x E. camaldulensis clone from 1-2m above ground level. Collected at 22:00.


title: Helper-dependent adenovirus vector treated animal #1 vs mock treated: 4 weeks post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30398.gif


title: Adeno-associated virus vector treated animal #2 vs mock: 1 hour post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37963.gif

source_name: Mock treated animal liver: 1 hour post-treatment

value: mock treated - 1 hour post-treatment

source_name: Adeno-associated virus vector treated animal liver: 1 hour post-treatment

value: adeno-associated virus vector treated - 1 hour post-treatment


title: GCEucXylem_TimeSeries_Slide12


title: Adenovirus vector treated animal #2 vs mock treated: 72 hours post-treatment

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30400.gif

value: mock treated - 72 hours post-treatment


title: Helper-dependent adenovirus vector treated animal #2 vs mock: 6 hours post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38379.gif

value: liver


title: Helper-dependent adenovirus vector treated animal #2 vs mock: 72 hrs post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37931.gif

source_name: Helper-dependent adenovirus vector treated animal liver: 72 hours post-treatment

value: helper-dependent adenovirus vector treated - 72 hours post-treatment


title: ectopic endometrium (endometrioma)

description:
Methylated DNA immunoprecipitation.
2_OME

source_name: endometrioma

value: endometriotic lesions (endometriomas)


title: Adeno-associated virus vector treated animal #1 vs mock treated: 4 weeks post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30389.gif

source_name: Adeno-associated virus vector treated animal liver: 4 weeks post-treatment

value: adeno-associated virus vector treated - 4 weeks post-treatment


title: GCEucXylem_TimeSeries_Slide11


title: eutopic endometrium

description:
Methylated DNA immunoprecipitation.
1_E

source_name: endometrium

value: Pool of 15 patients

value: endometrium control


title: Adeno-associated virus vector treated animal #1 vs mock treated: 72 hours post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31830.gif


title: Helper-dependent adenovirus vector treated animal #2 vs mock treated: 72 hours post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30465.gif


title: GCEucXylem_TimeSeries_Slide10


title: Adeno-associated virus vector treated animal #2 vs mock treated: 72 hours post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/31831.gif


title: Adeno-associated virus vector treated animal #2 vs mock : 4 weeks post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/38327.gif

value: mock treated - 4 weeks post-treatment


title: Helper-dependent adenovirus vector treated animal #1 vs mock: 72 hrs post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37928.gif


title: Adeno-associated virus vector treated animal #2 vs mock treated: 4 weeks post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30393.gif


title: GCEucXylem_TimeSeries_Slide8


title: Adenovirus vector treated animal #2 vs mock treated: 4 weeks post-treatment

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30397.gif

source_name: Adenovirus vector treated animal liver: 4 weeks post-treatment

value: adenovirus vector treated - 4 weeks post-treatment


title: Adeno-associated virus vector treated animal #1 vs mock treated: 6 hours post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29237.gif

value: mock treated - 6 hours post-treatment

source_name: Adeno-associated virus vector treated animal liver: 6 hours post-treatment

value: adeno-associated virus vector treated - 6 hours post-treatment


title: Helper-dependent adenovirus vector treated animal #1 vs mock treated: 1 hour post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41888.gif

source_name: Helper-dependent adenovirus vector treated animal liver: 1 hour post-treatment

value: helper-dependent adenovirus vector treated - 1 hour post-treatment


title: GCEucXylem_TimeSeries_Slide7


title: Adeno-associated virus vector treated animal #2 vs mock treated: 6 hours post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29344.gif

source_name: Mock treated animal liver: 6 hours post-treatment


title: GCEucXylem_TimeSeries_Slide5


title: miRNA-microarray-RNA2

city: San Antonio

first: Jonathan

middle: Adam

last: Gelfond

state: TX

address: Mail Code 7933, 7703 Floyd Curl

department: Epidemiology & Biostatistics

institute: UT Health Science Ctr San Antonio

description: technichal replicate 2 of 2.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump. Hybridization solution consisted of 100 µL of 6× SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C. After hybridization, the miRNAs were detected by fluorescence labeling using tag-specific Cy3 (single-color hybridization).

scan_protocol: Scanned on a GenePix 4000B (Molecular Device) laser scanner Images were quantified using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data was processed by subtracting the background and normalizing the signals using a Locally-weighted Regression filter by 5S rRNA. A miRNA was listed as a detectable when it met at least three criteria: 1) signal intensity higher than 3× the background standard deviation, 2) spot coefficient of variation (CV) < 0.5, in which CV was calculated as (standard deviation)/(signal intensity), and 3) at least 50% of the repeated probes had a signal 3-times higher than background standard deviation. The miRNA microarray data used the total gene signal, which was proportional to the total number of targets bound by the probes targeting each miRNA.

source_name: proliferating C2C12 cells

label_protocol: The assay started with 8 µg of total RNA sample. The RNA was size-fractionated using a YM-100 Microcon centrifugal filter (GE Millipore), and the 3′ ends of the small RNAs (<300 nt) were extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

growth_protocol: Mouse C2C12 myoblasts were cultured in growth media containing Dulbecco's Modified Eagle Medium (DMEM) (ATCC), supplemented with 10% fetal bovine serum (FBS) (Hyclone, Logan, UT) and 1% penicillin-streptomycin (Mediatech, Inc., Herndon, VA) at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol: Total RNA was isolated from proliferating C2C12 cells using TRIzol (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. Total RNA concentration was quantified by an absorbance at 260 nm using a SmartSpec 3000 spectrophotometer (Bio-Rad, Hercules, CA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and samples with RNA integrity number (RIN) >9 were used in the array studies. Aliquots of the same RNA sample were used for all the experiments in both the microarray and qPCR-array measurements.

value: muscle

tag: strain

tag: cell type

value: myoblast


title: Adeno-associated virus vector treated animal #2 vs mock treated: 1 hour post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-11/34831.gif


title: Adenovirus vector treated animal #1 vs mock treated: 4 weeks post-treatment

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30396.gif


title: Day1-RT1-ArrayA

description: Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

data_processing: Data was processed using SDS 2.3 software (Applied Biosystems, Foster City, CA). Normalized by subtracting mammu6 to get Delta CT

label: FAM

source_name: Proliferating C2C12 cells

tag: time

value: day 1

value: aliquot 1


title: Adenovirus vector treated animal #2 vs mock treated: 72 hours post-treatment: technical replicate

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37927.gif

source_name: Mock treated animal liver: 72 hours post-treatment

source_name: Adenovirus vector treated animal liver: 72 hours post-treatment

value: adenovirus vector treated - 72 hours post-treatment


title: NonAmp1_ArrayB

tag: protocol

value: no amplification


title: miRNA-microarray-RNA1

description: technichal replicate 1 of 2.


title: Adenovirus vector treated animal #1 vs mock treated: 6 hours post-treatment: technical replicate

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-03/38380.gif

tag: treatment

value: liver

source_name: Adenovirus vector treated animal liver: 6 hours post-treatment

value: adenovirus vector treated - 6 hours post-treatment


title: CFW RPL16a-ZZ total vs reference (1)

status: Public on May 12 2009

city: ETH Hoenggerberg, Zuerich

first: Andre

last: Gerber

address: Wolfgang Pauli Str. 10, HCI H396

department: Institute of Pharmaceutical Science

country: Switzerland

institute: Swiss Federal Institute of Technology

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-01/66391.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 19360; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 9244; Parameter Laser Power = 3.10; Parameter Scan Time = 10:14:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-01-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 370; Parameter Scan Power = 100; Parameter Laser on time = 9244; Parameter Laser Power = 3.59; Parameter Scan Time = 10:14:48; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.00; Performer: Regula,,Halbeisen

organism: Saccharomyces cerevisiae

source_name: Reference RNA

tag: Reference RNA

source_name: Total RNA RPL16a-ZZ

tag: Total RNA RPL16a-ZZ


title: Sorbitol RPL16a-ZZ IP poly vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70538.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2680, 19320; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 370; Parameter Laser on time = 14950; Parameter Laser Power = 2.95; Parameter Scan Time = 12:02:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 350; Parameter Scan Power = 100; Parameter Laser on time = 14950; Parameter Laser Power = 3.60; Parameter Scan Time = 12:02:50; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ

tag: IP RNA RPL16a-ZZ


title: Adeno-associated virus vector treated animal #1 vs mock treated: 1 hour post-treatment

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37962.gif

source_name: Mock treated animal liver: 1 hour post-treatment

value: mock treated - 1 hour post-treatment

tag: tissue

source_name: Adeno-associated virus vector treated animal liver: 1 hour post-treatment

value: adeno-associated virus vector treated - 1 hour post-treatment


title: Helper-dependent adenovirus vector treated animal #1 vs mock treated: 72 hours post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-07/30442.gif

value: mock treated - 72 hours post-treatment

source_name: Helper-dependent adenovirus vector treated animal liver: 72 hours post-treatment

value: helper-dependent adenovirus vector treated - 72 hours post-treatment


title: Adeno-associated virus vector treated animal #2 vs mock: 72 hours post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-05/41254.gif

source_name: Adeno-associated virus vector treated animal liver: 72 hours post-treatment

value: adeno-associated virus vector treated - 72 hours post-treatment


title: Sorbitol  RPL16a-ZZ IP poly vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70015.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 760, 20040; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 420; Parameter Laser on time = 14422; Parameter Laser Power = 2.98; Parameter Scan Time = 15:14:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.75; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 370; Parameter Scan Power = 100; Parameter Laser on time = 14422; Parameter Laser Power = 3.62; Parameter Scan Time = 15:14:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.75; Performer: Regula,,Halbeisen


title: Sorbitol RPL16a-ZZ total vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70642.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1600, 19960; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 15368; Parameter Laser Power = 2.93; Parameter Scan Time = 13:31:49; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 320; Parameter Scan Power = 100; Parameter Laser on time = 15368; Parameter Laser Power = 3.61; Parameter Scan Time = 13:31:49; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen


title: Menadione RPL16a-ZZ IP poly vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70539.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2560, 19440; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 360; Parameter Laser on time = 14971; Parameter Laser Power = 2.96; Parameter Scan Time = 12:23:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 14971; Parameter Laser Power = 3.60; Parameter Scan Time = 12:23:44; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.00; Performer: Regula,,Halbeisen


title: Adeno-associated virus vector treated animal #1 vs mock : 4 weeks post-treatment: tech replicate

description:
Simple annotation: Gene therapy, Adeno-associated virus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37964.gif

source_name: Mock treated animal liver: 4 weeks post-treatment

value: mock treated - 4 weeks post-treatment

source_name: Adeno-associated virus vector treated animal liver: 4 weeks post-treatment

value: adeno-associated virus vector treated - 4 weeks post-treatment


title: AAs starvation RPL16a-ZZ IP poly vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66122.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 19720; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 540; Parameter Laser on time = 9103; Parameter Laser Power = 3.14; Parameter Scan Time = 13:58:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 9102; Parameter Laser Power = 3.61; Parameter Scan Time = 13:58:20; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ AAs starvation

tag: IP RNA RPL16a-ZZ AAs starvation


title: AAs starvation RPL16a-ZZ total vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67971.gif
Measurement: time(absolute) 10 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 840, 19680; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 10177; Parameter Laser Power = 3.06; Parameter Scan Time = 12:06:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 350; Parameter Scan Power = 100; Parameter Laser on time = 10177; Parameter Laser Power = 3.56; Parameter Scan Time = 12:06:56; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.00; Performer: Regula,,Halbeisen

source_name: Total RNA AA-starved cells

tag: Total RNA AA-starved cells


title: CFW RPL16a-ZZ total vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68678.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 20080; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 11851; Parameter Laser Power = 2.90; Parameter Scan Time = 10:25:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 11851; Parameter Laser Power = 3.60; Parameter Scan Time = 10:25:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen

source_name: total RNA CFW

tag: total RNA CFW


title: AAs starvation RPL16a-ZZ total vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67167.gif
Measurement: time(absolute) 10 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 19840; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 440; Parameter Laser on time = 9611; Parameter Laser Power = 3.12; Parameter Scan Time = 10:31:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 9611; Parameter Laser Power = 3.54; Parameter Scan Time = 10:31:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.94; Performer: Regula,,Halbeisen


title: Adenovirus vector treated animal #2 vs mock treated: 1 hour post-treatment

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41870.gif

source_name: Adenovirus vector treated animal liver: 1 hour post-treatment

value: adenovirus vector treated - 1 hour post-treatment


title: Adenovirus vector treated animal #2 vs mock treated: 6 hours post-treatment

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2002-05/29335.gif

source_name: Mock treated animal liver: 6 hours post-treatment

value: mock treated - 6 hours post-treatment


title: Helper-dependent adenovirus vector treated animal #2 vs mock treated: 1 hour post-treatment

description:
Simple annotation: Gene therapy, Helper dependent adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41889.gif

source_name: Helper-dependent adenovirus vector treated animal liver: 1 hour post-treatment

value: helper-dependent adenovirus vector treated - 1 hour post-treatment


title: AAs starvation RPL16a-ZZ IP poly vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68679.gif
Measurement: time(absolute) 10 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 20080; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 11882; Parameter Laser Power = 2.92; Parameter Scan Time = 10:55:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.13; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 390; Parameter Scan Power = 100; Parameter Laser on time = 11882; Parameter Laser Power = 3.61; Parameter Scan Time = 10:55:57; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.13; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ AA-starved

tag: IP RNA RPL16a-ZZ AA-starved


title: Menadione RPL16a-ZZ total vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70588.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 19640; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 15236; Parameter Laser Power = 2.91; Parameter Scan Time = 11:19:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-06; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15235; Parameter Laser Power = 3.61; Parameter Scan Time = 11:19:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.81; Performer: Regula,,Halbeisen


title: CFW RPL16a-ZZ total vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67972.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1320, 19600; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 430; Parameter Laser on time = 10194; Parameter Laser Power = 3.07; Parameter Scan Time = 12:23:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.19; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 10194; Parameter Laser Power = 3.59; Parameter Scan Time = 12:23:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.19; Performer: Regula,,Halbeisen


title: RPL16a-ZZ IP poly vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66119.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1040, 20040; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 9012; Parameter Laser Power = 3.14; Parameter Scan Time = 12:27:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 490; Parameter Scan Power = 100; Parameter Laser on time = 9012; Parameter Laser Power = 3.61; Parameter Scan Time = 12:27:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen

source_name: RPL16a-ZZ IP RNA

tag: RPL16a-ZZ IP RNA


title: AAs starvation RPL16a-ZZ total vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68676.gif
Measurement: time(absolute) 10 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1400, 19840; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 11837; Parameter Laser Power = 2.90; Parameter Scan Time = 10:10:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.81; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 350; Parameter Scan Power = 100; Parameter Laser on time = 11837; Parameter Laser Power = 3.60; Parameter Scan Time = 10:10:55; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.81; Performer: Regula,,Halbeisen

source_name: Reference RNA


title: CFW100 RPL16a-ZZ IP poly vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70537.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 2720, 19720; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 370; Parameter Laser on time = 15045; Parameter Laser Power = 2.95; Parameter Scan Time = 13:37:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15044; Parameter Laser Power = 3.63; Parameter Scan Time = 13:37:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen


title: RPL16a-ZZ IP poly vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67015.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 920, 18800; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 440; Parameter Laser on time = 9396; Parameter Laser Power = 3.09; Parameter Scan Time = 11:56:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.31; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 500; Parameter Scan Power = 100; Parameter Laser on time = 9396; Parameter Laser Power = 3.57; Parameter Scan Time = 11:56:31; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.31; Performer: Regula,,Halbeisen


title: Adenovirus vector treated animal #1 vs mock treated: 72 hours post-treatment: technical replicate

description:
Simple annotation: Gene therapy, Adenovirus
Image: http://smd.stanford.edu/MicroArray/gifs/2003-02/37926.gif

scan_protocol: GenePix

source_name: Mock treated animal liver: 72 hours post-treatment

source_name: Adenovirus vector treated animal liver: 72 hours post-treatment


title: CFW100 RPL16a-ZZ IP poly vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70012.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 19880; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 14394; Parameter Laser Power = 2.98; Parameter Scan Time = 14:46:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 14393; Parameter Laser Power = 3.63; Parameter Scan Time = 14:46:08; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ


title: CFW100 RPL16a-ZZ total vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70535.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 840, 19440; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 14880; Parameter Laser Power = 2.91; Parameter Scan Time = 10:52:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 390; Parameter Scan Power = 100; Parameter Laser on time = 14880; Parameter Laser Power = 3.60; Parameter Scan Time = 10:52:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen

source_name: total RNA RPL16a-ZZ

tag: total RNA RPL16a-ZZ


title: AAs starvation RPL16a-ZZ IP poly vs reference (5)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69656.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 920, 20720; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 370; Parameter Laser on time = 13904; Parameter Laser Power = 2.82; Parameter Scan Time = 11:18:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.56; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 410; Parameter Scan Power = 100; Parameter Laser on time = 13903; Parameter Laser Power = 3.58; Parameter Scan Time = 11:18:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.56; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ AA20'

tag: IP RNA RPL16a-ZZ AA20'


title: AAs starvation RPL16a-ZZ IP poly vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, AA_starvation
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67017.gif
Measurement: time(absolute) 10 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 840, 19360; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 460; Parameter Laser on time = 9411; Parameter Laser Power = 3.11; Parameter Scan Time = 12:11:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.38; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 440; Parameter Scan Power = 100; Parameter Laser on time = 9411; Parameter Laser Power = 3.58; Parameter Scan Time = 12:11:28; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.38; Performer: Regula,,Halbeisen


title: CFW100 RPL16a-ZZ total vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70717.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1880, 20000; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 15670; Parameter Laser Power = 2.95; Parameter Scan Time = 13:57:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.69; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15669; Parameter Laser Power = 3.57; Parameter Scan Time = 13:57:52; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.69; Performer: Regula,,Halbeisen

source_name: Total RNA RPL16a-ZZ


title: CFW RPL16a-ZZ IP poly vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-02/67018.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 19320; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 560; Parameter Laser on time = 9431; Parameter Laser Power = 3.12; Parameter Scan Time = 12:31:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.50; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-02-10; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 9431; Parameter Laser Power = 3.58; Parameter Scan Time = 12:31:24; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.50; Performer: Regula,,Halbeisen


title: CFW RPL16a-ZZ IP poly vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67976.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 19880; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 440; Parameter Laser on time = 10343; Parameter Laser Power = 3.09; Parameter Scan Time = 14:52:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 350; Parameter Scan Power = 100; Parameter Laser on time = 10343; Parameter Laser Power = 3.60; Parameter Scan Time = 14:52:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen

source_name: IP RNA RPL16a-ZZ CFW

tag: IP RNA RPL16a-ZZ CFW


title: Menadione RPL16a-ZZ IP poly vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70013.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 19840; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 14408; Parameter Laser Power = 2.97; Parameter Scan Time = 14:59:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 14407; Parameter Laser Power = 3.62; Parameter Scan Time = 14:59:58; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.94; Performer: Regula,,Halbeisen


title: RPL16a-ZZ IP poly vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-04/67974.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 19640; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 380; Parameter Laser on time = 10329; Parameter Laser Power = 3.08; Parameter Scan Time = 14:38:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.88; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-04-04; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 470; Parameter Scan Power = 100; Parameter Laser on time = 10329; Parameter Laser Power = 3.60; Parameter Scan Time = 14:38:43; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.88; Performer: Regula,,Halbeisen


title: Menadione RPL16a-ZZ total vs reference (2)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70536.gif
Measurement: time(absolute) 20 m
Growth Condition: Menadione

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 19480; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 430; Parameter Laser on time = 14894; Parameter Laser Power = 2.92; Parameter Scan Time = 11:06:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.44; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-09-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 370; Parameter Scan Power = 100; Parameter Laser on time = 14894; Parameter Laser Power = 3.59; Parameter Scan Time = 11:06:36; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.44; Performer: Regula,,Halbeisen


title: CFW RPL16a-ZZ IP poly vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-05/68680.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 20080; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 450; Parameter Laser on time = 11896; Parameter Laser Power = 2.93; Parameter Scan Time = 11:10:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.31; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-05-26; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 420; Parameter Scan Power = 100; Parameter Laser on time = 11896; Parameter Laser Power = 3.60; Parameter Scan Time = 11:10:04; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.31; Performer: Regula,,Halbeisen


title: CFW100 RPL16a-ZZ total vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-09/70009.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 680, 20120; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 14351; Parameter Laser Power = 2.97; Parameter Scan Time = 14:03:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.75; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-29; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 330; Parameter Scan Power = 100; Parameter Laser on time = 14351; Parameter Laser Power = 3.60; Parameter Scan Time = 14:03:34; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.75; Performer: Regula,,Halbeisen


title: RPL16a-ZZ total vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2005-12/66118.gif
Measurement: time(absolute) 0 m
Growth Condition: none

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 19680; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 410; Parameter Laser on time = 8974; Parameter Laser Power = 3.11; Parameter Scan Time = 11:49:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.38; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2005-12-20; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 350; Parameter Scan Power = 100; Parameter Laser on time = 8974; Parameter Laser Power = 3.60; Parameter Scan Time = 11:49:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.38; Performer: Regula,,Halbeisen


title: CFW100 RPL16a-ZZ IP poly vs reference (4)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70716.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1760, 19600; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 15619; Parameter Laser Power = 2.96; Parameter Scan Time = 09:56:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 360; Parameter Scan Power = 100; Parameter Laser on time = 15619; Parameter Laser Power = 3.60; Parameter Scan Time = 09:56:19; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.25; Performer: Regula,,Halbeisen


title: AAs starvation RPL16a-ZZ total vs reference (6)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70713.gif
Measurement: time(absolute) 20 m
Growth Condition: Amino acid starvation

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1840, 19680; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 390; Parameter Laser on time = 15579; Parameter Laser Power = 2.95; Parameter Scan Time = 09:16:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15579; Parameter Laser Power = 3.61; Parameter Scan Time = 09:16:25; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 23.75; Performer: Regula,,Halbeisen


title: CFW100 RPL16a-ZZ IP poly vs reference (3)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70715.gif
Measurement: time(absolute) 20 m
Growth Condition: CFW

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1720, 20000; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 380; Parameter Laser on time = 15606; Parameter Laser Power = 2.96; Parameter Scan Time = 09:43:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-10-17; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 340; Parameter Scan Power = 100; Parameter Laser on time = 15606; Parameter Laser Power = 3.61; Parameter Scan Time = 09:43:29; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 24.06; Performer: Regula,,Halbeisen


title: Sorbitol RPL16a-ZZ IP poly  vs reference (1)

description:
Simple annotation: RNA coimmunoprecipitation, Condition media
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69658.gif
Measurement: time(absolute) 10 m
Growth Condition: Sorbitol

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 800, 20320; Software: type: feature extraction; Performer: Regula,,Halbeisen Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Pixel Size = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 100; Parameter PMT Volts = 400; Parameter Laser on time = 13920; Parameter Laser Power = 2.83; Parameter Scan Time = 11:31:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.63; Performer: Regula,,Halbeisen Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scan Date = 2006-08-09; Parameter Scanning software = AxImageIO; Parameter Scanning software version = 2.0.3.1; Parameter Pixel Size = 10; Parameter PMT Volts = 430; Parameter Scan Power = 100; Parameter Laser on time = 13920; Parameter Laser Power = 3.61; Parameter Scan Time = 11:31:53; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scanner Model = GenePix 4200A 01 [99046]; Parameter Focus Position = 0; Parameter Scan Temperature = 25.63; Performer: Regula,,Halbeisen